NeuroVault meta-analysis of stop-go paradigm studies#

This example shows how to download statistical maps from Neurovault.

See nilearn.datasets.fetch_neurovault_ids documentation for more details.

import scipy

from nilearn import plotting
from nilearn.datasets import fetch_neurovault_ids
from nilearn.image import get_data, load_img, math_img, new_img_like

Fetch images for “successful stop minus go”-like protocols.#

# These are the images we are interested in,
# in order to save time we specify their ids explicitly.
stop_go_image_ids = (151, 3041, 3042, 2676, 2675, 2818, 2834)

# These ids were determined by querying Neurovault like this:

# from nilearn.datasets import fetch_neurovault, neurovault
#
# nv_data = fetch_neurovault(
#     max_images=7,
#     cognitive_paradigm_cogatlas=neurovault.Contains('stop signal'),
#     contrast_definition=neurovault.Contains('succ', 'stop', 'go'),
#     map_type='T map')
#
# print([meta['id'] for meta in nv_data['images_meta']])

nv_data = fetch_neurovault_ids(image_ids=stop_go_image_ids)

images_meta = nv_data["images_meta"]
Reading local neurovault data.
Already fetched 1 image
Already fetched 2 images
Already fetched 3 images
Already fetched 4 images
Already fetched 5 images
Already fetched 6 images
Already fetched 7 images
7 images found on local disk.

Visualize the data#

print("\nplotting glass brain for collected images\n")

for im in images_meta:
    plotting.plot_glass_brain(
        im["absolute_path"],
        title=f"image {im['id']}: {im['contrast_definition']}",
    )
  • plot neurovault meta analysis
  • plot neurovault meta analysis
  • plot neurovault meta analysis
  • plot neurovault meta analysis
  • plot neurovault meta analysis
  • plot neurovault meta analysis
  • plot neurovault meta analysis
plotting glass brain for collected images

Compute statistics#

def t_to_z(t_scores, deg_of_freedom):
    """Convert t-scores to z-scores."""
    p_values = scipy.stats.t.sf(t_scores, df=deg_of_freedom)
    z_values = scipy.stats.norm.isf(p_values)
    return z_values


# Compute z values
z_imgs = []
current_collection = None

print("\nComputing maps...")

# convert t to z for all images
for this_meta in images_meta:
    if this_meta["collection_id"] != current_collection:
        print(f"\n\nCollection {this_meta['id']}:")
        current_collection = this_meta["collection_id"]

    # Load and validate the downloaded image.
    t_img = load_img(this_meta["absolute_path"])
    deg_of_freedom = this_meta["number_of_subjects"] - 2
    print(
        f"     Image {this_meta['id']}: degrees of freedom: {deg_of_freedom}"
    )

    # Convert data, create new image.
    z_img = new_img_like(
        t_img, t_to_z(get_data(t_img), deg_of_freedom=deg_of_freedom)
    )

    z_imgs.append(z_img)
Computing maps...


Collection 3042:
     Image 3042: degrees of freedom: 22


Collection 2676:
     Image 2676: degrees of freedom: 6
     Image 2675: degrees of freedom: 6


Collection 2818:
     Image 2818: degrees of freedom: 18
     Image 2834: degrees of freedom: 18


Collection 3041:
     Image 3041: degrees of freedom: 13
     Image 151: degrees of freedom: 13

Plot the combined z maps#

cut_coords = [-15, -8, 6, 30, 46, 62]
meta_analysis_img = math_img(
    "np.sum(z_imgs, axis=3) / np.sqrt(z_imgs.shape[3])", z_imgs=z_imgs
)

plotting.plot_stat_map(
    meta_analysis_img,
    display_mode="z",
    threshold=6,
    cut_coords=cut_coords,
    vmax=12,
)

plotting.show()
plot neurovault meta analysis

Total running time of the script: (0 minutes 12.664 seconds)

Estimated memory usage: 58 MB

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